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Items: 35

1.

RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data.

Ernlund AW, Schneider RJ, Ruggles KV.

BMC Genomics. 2018 Nov 8;19(1):809. doi: 10.1186/s12864-018-5166-z.

2.

Evaluating Alternative Designs of a Multilevel HIV Intervention in Maharashtra, India: The Impact of Stakeholder Constraints.

Patel AR, Ruggles KV, Nucifora K, Zhou Q, Schensul S, Schensul J, Bryant K, Braithwaite RS.

MDM Policy Pract. 2018 Oct 16;3(2):2381468318803940. doi: 10.1177/2381468318803940. eCollection 2018 Jul-Dec.

3.

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village.

Ruggles KV, Wang J, Volkova A, Contreras M, Noya-Alarcon O, Lander O, Caballero H, Dominguez-Bello MG.

mSphere. 2018 Aug 29;3(4). pii: e00193-18. doi: 10.1128/mSphere.00193-18.

4.

Loss of HDAC6 alters gut microbiota and worsens obesity.

Lieber AD, Beier UH, Xiao H, Wilkins BJ, Jiao J, Li XS, Schugar RC, Strauch CM, Wang Z, Brown JM, Hazen SL, Bokulich NA, Ruggles KV, Akimova T, Hancock WW, Blaser MJ.

FASEB J. 2019 Jan;33(1):1098-1109. doi: 10.1096/fj.201701586R. Epub 2018 Aug 13.

PMID:
30102568
5.

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity.

Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ.

Elife. 2018 Jul 25;7. pii: e37816. doi: 10.7554/eLife.37816.

6.

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.

Devlin JC, Battaglia T, Blaser MJ, Ruggles KV.

BMC Genomics. 2018 Jun 25;19(1):493. doi: 10.1186/s12864-018-4870-z.

7.

Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers.

Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX.

Cancer Res. 2018 May 15;78(10):2732-2746. doi: 10.1158/0008-5472.CAN-17-1990. Epub 2018 Feb 22.

8.

Heroin Use and Drug Injection among Youth Also Misusing Prescription Drugs.

Rajan S, Ruggles KV, Guarino H, Mateu-Gelabert P.

Am J Health Behav. 2018 Jan 1;42(1):144-155. doi: 10.5993/AJHB.42.1.14.

9.

Betting on the fastest horse: Using computer simulation to design a combination HIV intervention for future projects in Maharashtra, India.

Ruggles KV, Patel AR, Schensul S, Schensul J, Nucifora K, Zhou Q, Bryant K, Braithwaite RS.

PLoS One. 2017 Sep 5;12(9):e0184179. doi: 10.1371/journal.pone.0184179. eCollection 2017.

10.

Bacteriophages as potential new mammalian pathogens.

Tetz GV, Ruggles KV, Zhou H, Heguy A, Tsirigos A, Tetz V.

Sci Rep. 2017 Aug 1;7(1):7043. doi: 10.1038/s41598-017-07278-6.

11.

Methods, Tools and Current Perspectives in Proteogenomics.

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR.

Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29. Review.

12.

Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA, Ellis MJ, Ding L.

Nat Commun. 2017 Apr 25;8:15479. doi: 10.1038/ncomms15479. No abstract available.

13.

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L.

Nat Commun. 2017 Mar 28;8:14864. doi: 10.1038/ncomms14864.

14.

Sexual Risk and Transmission Behaviors, Partnerships and Settings Among Young Adult Nonmedical Opioid Users in New York City.

Friedman SR, Mateu-Gelabert P, Ruggles KV, Goodbody E, Syckes C, Jessell L, Teubl J, Guarino H.

AIDS Behav. 2017 Apr;21(4):994-1003. doi: 10.1007/s10461-016-1672-7.

15.

Next Generation Sequencing Data and Proteogenomics.

Ruggles KV, Fenyö D.

Adv Exp Med Biol. 2016;926:11-19. Review.

PMID:
27686803
16.

What are the Patterns Between Depression, Smoking, Unhealthy Alcohol Use, and Other Substance Use Among Individuals Receiving Medical Care? A Longitudinal Study of 5479 Participants.

Ruggles KV, Fang Y, Tate J, Mentor SM, Bryant KJ, Fiellin DA, Justice AC, Braithwaite RS.

AIDS Behav. 2017 Jul;21(7):2014-2022. doi: 10.1007/s10461-016-1492-9.

17.

Proteogenomics connects somatic mutations to signalling in breast cancer.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC.

Nature. 2016 Jun 2;534(7605):55-62. doi: 10.1038/nature18003. Epub 2016 May 25.

18.

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG.

Methods Mol Biol. 2016;1410:223-36. doi: 10.1007/978-1-4939-3524-6_13.

19.

PGx: Putting Peptides to BED.

Askenazi M, Ruggles KV, Fenyö D.

J Proteome Res. 2016 Mar 4;15(3):795-9. doi: 10.1021/acs.jproteome.5b00870. Epub 2015 Dec 18.

20.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyő D.

Mol Cell Proteomics. 2016 Mar;15(3):1060-71. doi: 10.1074/mcp.M115.056226. Epub 2015 Dec 2.

21.

Characteristics of the most viewed YouTube™ videos related to bullying.

Basch CH, Ruggles KV, Berdnik A, Basch CE.

Int J Adolesc Med Health. 2015 Nov 10;29(4). pii: /j/ijamh.2017.29.issue-4/ijamh-2015-0063/ijamh-2015-0063.xml. doi: 10.1515/ijamh-2015-0063.

PMID:
26556842
22.

Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts.

Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyö D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL.

Mol Cell Proteomics. 2016 Jan;15(1):45-56. doi: 10.1074/mcp.M114.047480. Epub 2015 Oct 26.

23.

Profiling the Essential Nature of Lipid Metabolism in Asexual Blood and Gametocyte Stages of Plasmodium falciparum.

Gulati S, Ekland EH, Ruggles KV, Chan RB, Jayabalasingham B, Zhou B, Mantel PY, Lee MC, Spottiswoode N, Coburn-Flynn O, Hjelmqvist D, Worgall TS, Marti M, Di Paolo G, Fidock DA.

Cell Host Microbe. 2015 Sep 9;18(3):371-81. doi: 10.1016/j.chom.2015.08.003.

24.

Sexual Violence in the Context of Drug Use Among Young Adult Opioid Users in New York City.

Jessell L, Mateu-Gelabert P, Guarino H, Vakharia SP, Syckes C, Goodbody E, Ruggles KV, Friedman S.

J Interpers Violence. 2017 Oct;32(19):2929-2954. doi: 10.1177/0886260515596334. Epub 2015 Aug 3.

25.

ATP-binding cassette transporters and sterol O-acyltransferases interact at membrane microdomains to modulate sterol uptake and esterification.

Gulati S, Balderes D, Kim C, Guo ZA, Wilcox L, Area-Gomez E, Snider J, Wolinski H, Stagljar I, Granato JT, Ruggles KV, DeGiorgis JA, Kohlwein SD, Schon EA, Sturley SL.

FASEB J. 2015 Nov;29(11):4682-94. doi: 10.1096/fj.14-264796. Epub 2015 Jul 28.

26.

Coverage of the Ebola Virus Disease Epidemic on YouTube.

Basch CH, Basch CE, Ruggles KV, Hammond R.

Disaster Med Public Health Prep. 2015 Oct;9(5):531-5. doi: 10.1017/dmp.2015.77. Epub 2015 Jun 19.

PMID:
26088275
27.

Aggressive and violent behaviors in the school environment among a nationally representative sample of adolescent youth.

Rajan S, Namdar R, Ruggles KV.

J Sch Health. 2015 Jul;85(7):446-57. doi: 10.1111/josh.12272.

PMID:
26032275
28.
29.

Gun possession among American youth: a discovery-based approach to understand gun violence.

Ruggles KV, Rajan S.

PLoS One. 2014 Nov 5;9(11):e111893. doi: 10.1371/journal.pone.0111893. eCollection 2014.

30.

Use of sunscreen and indoor tanning devices among a nationally representative sample of high school students, 2001-2011.

Basch CH, Basch CE, Rajan S, Ruggles KV.

Prev Chronic Dis. 2014 Aug 21;11:E144. doi: 10.5888/pcd11.140191.

31.

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.

Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA.

Mol Cell Proteomics. 2014 Jul;13(7):1690-704. doi: 10.1074/mcp.M113.036392. Epub 2014 Apr 9.

32.

A functional, genome-wide evaluation of liposensitive yeast identifies the "ARE2 required for viability" (ARV1) gene product as a major component of eukaryotic fatty acid resistance.

Ruggles KV, Garbarino J, Liu Y, Moon J, Schneider K, Henneberry A, Billheimer J, Millar JS, Marchadier D, Valasek MA, Joblin-Mills A, Gulati S, Munkacsi AB, Repa JJ, Rader D, Sturley SL.

J Biol Chem. 2014 Feb 14;289(7):4417-31. doi: 10.1074/jbc.M113.515197. Epub 2013 Nov 22.

33.

Making, baking, and breaking: the synthesis, storage, and hydrolysis of neutral lipids.

Ruggles KV, Turkish A, Sturley SL.

Annu Rev Nutr. 2013;33:413-51. doi: 10.1146/annurev-nutr-071812-161254. Epub 2013 May 22. Review.

PMID:
23701589
34.

Phosphatidate phosphatase activity plays key role in protection against fatty acid-induced toxicity in yeast.

Fakas S, Qiu Y, Dixon JL, Han GS, Ruggles KV, Garbarino J, Sturley SL, Carman GM.

J Biol Chem. 2011 Aug 19;286(33):29074-85. doi: 10.1074/jbc.M111.258798. Epub 2011 Jun 27.

35.

Sterol and diacylglycerol acyltransferase deficiency triggers fatty acid-mediated cell death.

Garbarino J, Padamsee M, Wilcox L, Oelkers PM, D'Ambrosio D, Ruggles KV, Ramsey N, Jabado O, Turkish A, Sturley SL.

J Biol Chem. 2009 Nov 6;284(45):30994-1005. doi: 10.1074/jbc.M109.050443. Epub 2009 Aug 18.

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